If I am looking at this correctly:
N with Zekrom/Reshiram faces off against Ghetsis and Kyurem.
Kyurem physically merges with Zekrom/Reshiram.
We battle the newly formed Kyurem fusion at level 55 after the initial encounter, and after defeating it, it loses its fusion forme.
After the story is over, we battle N who has re-obtained his Dragon at level 70.
After defeating him, he releases Zekrom/Reshiram who flies off to Dragon Spiral Tower, while Kyurem awaits in the giant Chasm.
After catching them both, we return to N's Castle to activate an event where they fuse back into BW Kyurem at level 70 and capture them.
Whoo! Does that sound about right?